\HeaderA{ScISI}{The In Silico Interactome for Saccharomyces cerevisiae}{ScISI}
\aliasA{ScISIC}{ScISI}{ScISIC}
\aliasA{ScISIverified}{ScISI}{ScISIverified}
\keyword{datasets}{ScISI}
\begin{Description}\relax
This is the incidence sparse-matrix representatin for the bi-partite graph
for the in silico interactome given by Saccharomyces cerevisiae. The
rows are indexed by the systematic gene names and the colunmns are
indexed by the protein complexes. This matrix contains a 1 in the
(i,j) postion if the protein in indexed in the i-th row is a member of
the protein complex of the j-th column; it contains a 0 otherwise.

ScISIC is a sub-interactome of ScISI which consists of protein complexes
derived from small scale experiments and have been curated by Gene Ontology (GO)
or MIPS. While these complexes have been curated, not all of them have
been completely verified to be true. Periodic changes to GO and MIPS 
will percolate through the protein complexes or protein complex composition
and so the ScISIC will need to be rebuilt. A script located in the 
inst/Scripts/ entitled createScISIC.R creates an updated ScISIC if the GO and
MIPS's files are up to date. GO 2.0.0 and complexcat-data-2006 (MIPS) were 
used to build ScISIC for Bioconductor 2.1 release of the package ScISI. Both are 
the most up to date versions of the repository as of 9 October 2007. In addition
to MIPS and GO, we have also incorporated protein complexes curated by the 
IntAct repository. The IntAct protein complexes are obtained from the 
complex data XML file obtained from IntAct via Rintact. 

In addition to the protein complexes found within MIPS and GO, ScISIC also
contains manually curated protein complexes obtained from IntAct. Because IntAct
has yet to version its release, the protein complexes were obtained on 25 May 2007. 

ScISIC replaces ScISIverified which has been deprecated.

ScISI combines ScISIC with protein complex estimates on the datasets
derived by Gavin et al (2002), Ho et al (2002), and Krogan et al (2004)
using the penalized algorithm found with apComplex
developed by Scholtens et al (2004).
\end{Description}
\begin{Usage}
\begin{verbatim}data(ScISI)\end{verbatim}
\end{Usage}
\begin{Format}\relax
The format of both the ScISI and ScISIC is a binary incidence matrix.  The rows 
are indexed by the gene locus names and the columns are indexed by the 
identification codes for the protein complexes based on the repository from
where they are obtained.
\end{Format}
\begin{Details}\relax
This is the working in silico interactome built for computational
experimentation. The data from which this interactome is built is from
the Intact, Gene Ontology, Mips, and estimated protein complexes from
apComplex.
\end{Details}
\begin{Source}\relax
http://www.geneontology.org
\end{Source}
\begin{References}\relax
http://www/bioconductor.org
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(ScISIC)
\end{ExampleCode}
\end{Examples}

